tissues or specimens which will be analyzed by LC-MS -MS for next clinical information generally are stored at a temperature of -80 degrees centigrade, what is the stability of frozen tissues used for protein expression? is degratation be able to occur for a long period storage? For proteomics, does use of FFPE ( Formalin fixed paraffin embeeded ) tissues provide more advantage when to compare with frozen tissues?
Dear Ihsan,
For stability of frozen tissues for protein expression, please see the following comprehensive review published in 2014:
Clin Biochem. Author manuscript; available in PMC 2015 Mar 1.
Published in final edited form as:
Clin Biochem. 2014 Mar; 47(0): 258–266.
Published online 2014 Jan 12. doi: 10.1016/j.clinbiochem.2014.01.002
PMCID: PMC3982909
NIHMSID: NIHMS562521
The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings
Maryam Shabihkhani,1 Gregory M. Lucey,1 Bowen Wei,1 Sergey Mareninov,1 Jerry J. Lou,1 Harry V. Vinters,1,3,4 Elyse J. Singer,2,3 Timothy F. Cloughesy,2,4 and William H. Yong1,3,4
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The publisher's final edited version of this article is available at Clin Biochem
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Abstract
Well preserved frozen biospecimens are ideal for evaluating the genome, transcriptome, and proteome. While papers reviewing individual aspects of frozen biospecimens are available, we present a current overview of experimental data regarding procurement, storage, and quality assurance that can inform the handling of frozen biospecimens. Frozen biospecimen degradation can be influenced by factors independent of the collection methodology including tissue type, premortem agonal changes, and warm ischemia time during surgery. Rapid stabilization of tissues by snap freezing immediately can mitigate artifactually altered gene expression and, less appreciated, protein phosphorylation profiles. Collection protocols may be adjusted for specific tissue types as cellular ischemia tolerance varies widely. If data is not available for a particular tissue type, a practical goal is snap freezing within 20 minutes. Tolerance for freeze-thaw events is also tissue type dependent. Tissue storage at −80°C can preserve DNA and protein for years but RNA can show degradation at 5 years. For −80°C freezers, aliquots frozen in RNAlater or similar RNA stabilizing solutions is a consideration. It remains unresolved as to whether storage at −150°C provides significant advantages relative to −80°C. Histologic quality assurance of tissue biospecimens is typically performed at the time of surgery but should also be conducted on the aliquot to be distributed because of tissue heterogeneity. Biobanking protocols for blood and its components are highly dependent on intended use and multiple collection tube types may be needed. Additional quality assurance testing should be dictated by the anticipated downstream applications.
Keywords: Biorepository, biobank, frozen, tissue, procurement, biospecimen
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982909/
To view the full publication, please see attached file.
Comparisons between the frozen method and FFPE can be found in the following publication:
J Histochem Cytochem. 2009 Sep; 57(9): 849–860.
doi: 10.1369/jhc.2009.953497
PMCID: PMC2728129
Protein Extraction of Formalin-fixed, Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass Spectrometry
Marshall S. Scicchitano, Deidre A. Dalmas, Rogely W. Boyce, Heath C. Thomas, and Kendall S. Frazier
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Abstract
Global mass spectrometry (MS) profiling and spectral count quantitation are used to identify unique or differentially expressed proteins and can help identify potential biomarkers. MS has rarely been conducted in retrospective studies, because historically, available samples for protein analyses were limited to formalin-fixed, paraffin-embedded (FFPE) archived tissue specimens. Reliable methods for obtaining proteomic profiles from FFPE samples are needed. Proteomic analysis of these samples has been confounded by formalin-induced protein cross-linking. The performance of extracted proteins in a liquid chromatography tandem MS format from FFPE samples and extracts from whole and laser capture microdissected (LCM) FFPE and frozen/optimal cutting temperature (OCT)–embedded matched control rat liver samples were compared. Extracts from FFPE and frozen/OCT–embedded livers from atorvastatin-treated rats were further compared to assess the performance of FFPE samples in identifying atorvastatin-regulated proteins. Comparable molecular mass representation was found in extracts from FFPE and OCT-frozen tissue sections, whereas protein yields were slightly less for the FFPE sample. The numbers of shared proteins identified indicated that robust proteomic representation from FFPE tissue and LCM did not negatively affect the number of identified proteins from either OCT-frozen or FFPE samples. Subcellular representation in FFPE samples was similar to OCT-frozen, with predominantly cytoplasmic proteins identified. Biologically relevant protein changes were detected in atorvastatin-treated FFPE liver samples, and selected atorvastatin-related proteins identified by MS were confirmed by Western blot analysis. These findings demonstrate that formalin fixation, paraffin processing, and LCM do not negatively impact protein quality and quantity as determined by MS and that FFPE samples are amenable to global proteomic analysis. (J Histochem Cytochem 57:849–860, 2009)
For more details, see attached file.
Hoping this will be helpful,
Rafik
Dear Rafik,
Thank you so much for your helping, certainly articles attached by you will be helpul for me.
Best regards..
İhsan YOZGAT
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